One big advantage of MATLAB over R is the quality of MATLAB documentation. R, being open source, suffers in this respect, a feature common to many open source projects.
R is, however, a very useful environment and language. It is widely used in the bioinformatics community and has many packages useful in this domain.
An alternative to R is Octave (http://www.gnu.org/software/octave/) which is very similar to MATLAB, it can run MATLAB scripts.